1. ALGORITHM TYPES Divide and Conquer, Dynamic Programming, Greedy, and Backtracking Note the general strategy from the examples The classification is neither exhaustive (there may be other “types”), nor mutually exclusive (one may combine)

2. In case the divide and conquer strategy can divide the problem at a very small level, and there are repetition of some calculations over some components One can apply a bottom up approach: calculate the smaller components first and then keep combining them until the highest level of the problem is solved. Draw the recursion tree of Fibonacci-series calculation, you will see example of such repetitive calculations f(n) = f(n-1) + f(n-2), for n>1; and f(n)=1 otherwise fib(n) calculation n = 1, 2, 3, 4, 5 fib = 1, 2, 3, 5, 8 PROBLEM 1: DYNAMIC PROGRAMMING STRATEGY

3. DYNAMIC PROGRAMMING STRATEGY (Continued) Recursive fib(n) if (n<=1) return 1; elsereturn (fib(n-1) + fib(n-2)). Time complexity: exponential, O(k n ) for some k>1.0 Iterative fibonacci(n) fib(0) = fib(1) = 1; for i=2 through n do fib(i) = fib(i-1) + fib(i-2); end for; return fib(n). Time complexity: O(n), Space complexity: O(n)

4. SpaceSaving-fibonacci(n) if (n<=1) return 1; int last=1, last2last=1, result=1; for i=2 through n do result = last + last2last; last2last = last; last=result end for; return result. Time complexity: O(n), Space complexity: O(1) DYNAMIC PROGRAMMING STRATEGY (Continued)

5. The recursive call recalculates fib(1) 5 times, fib(2) 3 times, fib(3) 2 times - in fib(5) calculation. The complexity is exponential. In iterative calculation we avoid repetition by storing the needed values in variables - complexity of order n. Dynamic Programming approach consumes more memory to store the result of calculations of lower levels for the purpose of calculating the next higher level. They are typically stored in a table. DYNAMIC PROGRAMMING STRATEGY (Continued)

6. Given a set of objects with (Weight, Profit) pair, and a Knapsack of limited weight capacity (M), find a subset of objects for the knapsack to maximize total profit P Sample Problem: Objects (wt, p) = {(2, 1), (3, 2), (9, 20), (5, 3)}. M=8 Exhaustive Algorithm: Try all subset of objects. How many? Problem 1: 0-1 Knapsack Problem (not in the book) {}: total=(0 lbs, $0) {(2,1)}: total =(2lbs, $1) … {(9,20): Illegal, total wt>8 … {(2,1), (3,2)}: =(5lbs, $3) … Total possibilities = 2 n For each object present or absent 0 or 1 A bit string is a good representation for a set, e.g. 000101100…. n-bits

7. DP uses a representation for optimal profit P(j, k): –for the first j objects considered (in any arbitrary but pre- ordering of objects) – with a variable knapsack limit k Develop the table for P(j, k) –with rows j =1 …n (#objects), and –for each row, go from k =0 …M (the KS limit) Finally P(n, M) gets the result 0-1 Knapsack Problem w->012345678 { }{ }000000000 {O 1 }00111… => 1 {O 1 O 2 }0012233… => 3 {O 1 O 2 O 3 } 001223345

8. 0-1 Knapsack Recurrence Formula for computing P The recurrence, for all k=0…M, j=0…N P(j, k) = (case 1) P(j-1, k), if w j >k, w j is weight of the j-th object; else P(j, k) = (case2) max{ P(j-1, k-w j )+p j, P(j-1, k) } –Explanation for the formula is quite intuitive Recurrence terminates: P(0, k)=0, P(j, 0)=0, for all k’s and j’s w->012345678 { }{ }000000000 {O 1 }001111111 {O 1 O 2 }001223333 {O 1 O 2 O 3 } 00122 P(3,7)= 4 Objects (wt, p) = {(2, 1), (3, 2), (5, 3)}. M=9

9. Recurrence -> recursive algorithm Input: Set of n objects with (w i, p i ) pairs, and knapsack limit M Output: Maximum profit P for subset of objects with total wt ≤ M Function P(j, k) 1.If j ≤ 0 or k ≤ 0 then return 0; //recursion termination 2.else 3.if w j >k then 4.return P(j-1, k) 5.else 6.return max{P(j-1, k-Wj) + pj, P(j-1, k)} End algorithm. Driver: call P(n, M), for given n objects & KS limit M. This is not table building: P’s are recursive functions Complexity: ? Exponential: O(2 n ) Why? Same reason as in Fibonacci number calculation: Repeats computing P’s

10. 0-1 Knapsack: Recursive call tree Objects (wt, p) = {(2, 1), (3, 2), (5, 3)}. M=8 w->012345678 { }{ }000000000 {O 1 }00111… => 1 {O 1 O 2 }0012233… => 3 {O 1 O 2 O 3 } 001223345 P(3,8) P(2,8-5)P(2,8) P(1,8) P(1,8-3)P(1,3-3) P(1,3) P(0,3-2)P(0,3) P(0,0-2) P(0,0) P(0,5-2)P(0,5) P(0,8-2) P(0,8) w 1 =2>0, not called Each leaf has w=0, and P(0,*) returns a value, 0 to the caller above

11. 0-1 Knapsack: recurrence -> DP algorithm Input: Set of n objects with (w i, p i ) pairs, and knapsack limit M Output: Maximum profit P for a subset of objects with total wt ≤M Algorithm DPks(j, k) 1.For all k, P(0, k) =0; For all j, P(j, 0) = 0; //initialize 2.For j=1 to n do 1.For k= 1 to M do 3.if w j >k then 4.P(j, k) = P(j-1, k) 5.else 6.P(j, k)= max{P(j-1, k-Wj) + pj, P(j-1, k)} End loops and algorithm Do not repeat the same computation, store them in a table and reuse Complexity: O(nM), pseudo-polynomial because M is an input value. If M=30.5 the table would be of size O(10nM), or if M=30.54 it would be O(100NM).

12. 0-1 Knapsack Problem (Example) Objects (wt, p) = {(2, 1), (3, 2), (5, 3)}. M=8 w->012345678 { }{ } 000000000 {O 1 } 00111… =>1 {O 1 O 2 } 0012233… =>3 {O 1 O 2 O 3 } 001223345 +2$ +0$ -5 lbs (2+3)$

13. What if M=9 Objects (wt, p) = {(2, 1), (3, 2), (5, 3)}. M=9 w->0123456789 { }{ } 0000000000 {O 1 } 0011111111 {O 1 O 2 } 0012233333 {O 1 O 2 O 3 } 0012233455 HOW TO FIND KNAPSACK CONTENT FROM TABLE? SPACE COMPLEXITY? -5 lbs (2+3)$

14. Memoisation algorithm: 0-1 knapsack Algorithm P(j, k) If j <= 0 or k < = 0 then return 0; //recursion termination else if Wj>k then y=A(j-1, k); if y<0 {y = P(j-1, k) ; A(j-1, k)=y}; // P( ) is a recursive call, A() is matrix return y else x=A(j-1, k-Wj); if x<0 {x = P(j-1, k-Wj) ; A(j-1, k-Wj)=x}; y=A (j-1, k); if y<0 {y = P(j-1, k) ; A(j-1, k)=y}; A (j, k) = max{x+ pj, y}; return max{x+ pj, y} End algorithm. Driver: Initialize a global matrix A(0->n, 0->M) with -1; call P(n, M) Complexity: ?

15. A chain of matrices to be multiplied: ABCD, – dimensions: A (5x1), B(1x4), C(4x3), and D(3x6). – Resulting matrix will be of size (5x6). # scalar (or integer) multiplications for (BC) is 1.4.3, –and the resulting matrix’s dimension is (1x3), 1 column and 3 rows. Problem 2: Ordering of Matrix-chain Multiplications

16. Ordering of Matrix-chain Multiplications A (5x1), B(1x4), C(4x3), and D(3x6) Multiple ways to multiply: –(A(BC))D, –((AB)C)D, –(AB)(CD), –A(B(CD)), –A((BC)D) –note: Resulting matrix would be the same –but the computation time may vary drastically Time depends on #scalar multiplications –In the case of (A(BC))D, it is = 1.4.3 + 5.1.3 + 5.3.6 = 117 –In the case (A(B(CD)), it is = 4.3.6 + 1.4.6 + 5.1.6 = 126 Our problem here is to find the best such ordering –An exhaustive search over all orderings is too expensive - Catalan number involving n!

17. For a sequence A 1...( A left....A right )...A n, we want to find the optimal break point for the parenthesized sequence. Calculate for ( r-l+1) number of cases and find the minimum: min{(A l...A i ) (A i+1... A r ), with l  i < r}, Recurrence for optimum scalar-multiplication: M(l, r) = min{M(l, i) + M(i+1, r) + row l.col i.col r, with l  i < r}. Termination: M(l, l) = 0 Recurrence for Ordering of Matrix-chain Multiplications r = 1 2 3 4 lft 101535(2)69(2) 201242 3024 40 Sample M(i,j):

18. Matrix-chain Recursive algorithm Recursive Algorithm M(l, r) 1.if r<= l then return 0; // Recurrence termination: no scalar-mult 2.else 3. return min{M(l, i) + M(i+1, r) + row l.col i.col r, 4.for l  i<r}; 5.end algorithm. Driver: call M(1, n) for the final answer.

19. Recurrence for optimum scalar-multiplication: M(l, r) = min{M(l, i) + M(i+1, r) + row l.col i.col r, with l  i < r}. To compute M(l,r), you need M(l,i) and M(i+1,r) available for ALL i’s E.g., For M(3,9), you need M(3,3), M(4,9), and M(3,4), M(5,9), … –Need to compute smaller size M’s first –Gradually increase size from 1, 2, 3, …, n Recurrence for Ordering of Matrix-chain Multiplications to Bottom-up Computation

20. Recurrence for optimum number of scalar-multiplications: M(l, r) = min{M(l, i) + M(i+1, r) + row l.col i.col r, with l  i < r}. Compute by increasing size : r-l+1=1, r-l+1=2, r-l+1=3, … r-l+1=n Start the calculation at the lowest level with two matrices, AB, BC, CD etc. –Really? –Where does the recurrence terminate? Then calculate for the triplets, ABC, BCD etc. And so on… Strategy for Ordering of Bottom-up Computation =0, for l==r

21. r = 1 2 3 4 l 101535(2)69(2) 201242 3024 40 Ordering of Matrix-chain Multiplications (Example) Pairs Triplets Singlet's

22. Matrix-chain DP-algorithm Input: list of pairwise dimensions of matrices Output: optimum number of scalar multiplications 1.for all 1  i  n do M(i,i) = 0; // diagonal elements 0 2.for size = 2 to n do// size of subsequence 3.for l =1 to n-size+1 do 4.r = l+size-1;//move along diagonal 5.M(l,r) = infinity; //minimizer 6.for i = l to r-1 do 7.x = M(l, i) + M(i+1, r) 8.+ row l.col i.col r; 9.if x < M(l, r) then M(l, r) = x; End. // Complexities?

23. r = 1 2 3 4 l 10 20 30 40 Ordering of Matrix-chain Multiplications (Example) Pairs Triplets 15 12 24 35(2) 42(?) 69(2) A 1 (5x3), A 2 (3x1), A 3 (1x4), A 4 (4x6). Calculation goes diagonally. COMPLEXITY? How do you find out the actual matrix ordering?

24. A 1 (5x3), A 2 (3x1), A 3 (1x4), A 4 (4x6). M(1,1) = M(2,2) = M(3,3) = M(4,4) = 0 M(1, 2) = M(1,1) + M(2,2) + 5.3.1 = 0 + 0 + 15. M(1, 3) = min{ i=1 M(1,1)+M(2,3)+5.3.4, i=2 M(1,2)+M(3,3)+5.1.4 } = min{72, 35} = 35(2) M(1,4) = min{ i=1 M(1,1)+M(2,4)+5.3.6, i=2 M(1,2)+M(3,4)+5.1.6, i=3 M(1,3)+M(4,4)+5.4.6} = min{132, 69, 155} = 69(2) 69 comes from the break-point i=2: (A 1.A 2 )(A 3.A 4 ) Recursively break the sub-parts if necessary, e.g., for (A 1 A 2 A 3 ) optimum is at i=2: (A 1.A 2 )A 3 DP Ordering of Matrix-chain Multiplications (Example)

25. r = 1 2 3 4 l 101535(2)69(2) 201242 3024 40 Ordering of Matrix-chain Multiplications (Example) Pairs Triplets A1 (5x3), A2 (3x1), A3 (1x4), A4 (4x6). For a chain of n matrices, Table size=O(n 2 ), computing for each entry=O(n): COMPLEXITY = O(n 2 *n) = O(n 3 ) A separate matrix I(i,j) keeping track of optimum i, for actual matrix ordering

26. Computing the actual break points I(i,j) r = 1 2 3 456 l 1--(2)(2)(3)(3) 2--(3)(3)(4) 3--(4)(4) 4-(3)(4) 5 - - - 6 - - - Then: (A 1..A 3 ) -> (A 1 A 2 )(A 3 ), & (A 4 …A 6 ) -> A 4 (A 5 A 6 ) ABCDEF -> (ABC)(DEF) -> ((AB)C) (D(EF)) Backtrack on this table: (A 1..A 3 )(A 4 …A 6 ) ABCDEF -> (ABC)(DEF)

27. Inductive Proof of Matrix-chain Recurrence Induction base: 1.if r< l then absurd case, there is no matrix to multiply: return 0; 2.If r = = l, then only one matrix, no multiplication: return 0 Inductive hypothesis: 1.For all size<k, and k≥1, assume M(l,r) returns correct optimum Note: size = r-l+1 Inductive step, for size=k: 1.Consider all possible ways to break up (l…r) chain, for l  i<r : 2.Make sure to compute and add the resulting pair of matrices multiplication: row l.col i.col r 3.Since M(l,i) and M(i+1,r) are correct smaller size optimums, as per hypothesis, min { M(l, i) + M(i+1, r) + row l.col i.col r, for l  i<r } is the correct return value for M(l,r)

28. Be careful with the correctness of the Recurrence behind Dynamic Programming Inductive step: 1.Consider all possible ways to break up (l…r) chain, for l  i<r : 2.Make sure to compute the resulting pair of matrices multiplication: row l.col i.col r 3.Since M(l,i) and M(i+1,r) are correct smaller size optimums, per hypothesis, min{M(l, i) + M(i+1, r) + row l.col i.col r, for l  i<r} is the correct return value for M(l,r) It is NOT always possible to combine smaller steps to the larger one. Addition, Multiplication are associative: 4+3+1+2+9 = (((4+3) +(1+2)) +9), but average(4,3,1,2,9) = av( av(av(4,3), av(1,2)), 9), NOT true DP needs the correct formulation of a Recurrence first, Then, bottom up combination such that smaller problems contributes to the larger ones

29. Problem 3: Optimal Binary Search Tree Binary Search Problem: Input: sorted objects, and key Output: the key’s index in the list, or ‘not found’ Binary Search on a Tree: Sorted list is organized as a binary tree –Recursively: each root t is l ≤t ≤r, where l is any left descendant and r is any right descendant Example sorted list of objects: A 2, A 3, A 4, A 7, A 9, A 10, A 13, A 15 Sample correct binary-search trees: A7A7 A3A3 A4A4 A2A2 A 10 A9A9 A 13 A 15 A1A1 A3A3 A4A4 A7A7 A9A9 A 10 A 13 A 15 There are many such correct trees

30. Problem 3: Optimal Binary Search Tree Problem: Optimal Binary-search Tree Organization Input: Sorted list, with element’s access frequency (how many times to be accessed/searched as a key over a period of time) Output: Optimal binary tree organization so that total cost is minimal Cost for accessing each object= frequency*access steps to the object in the tree) Number of Access steps for each node is its distance from the root, plus one. Example list sorted by object order (index of A): A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4) A3(5) A1(7) A2(10) A4(8) A5(4) Cost = 5*1 +7*2 + 10*3 +8*2 + 4*3 = 77 A1(7) A2(10) A3(5) A4(8) A5(4) Cost = 7*1 + 10*2 + 5*3 + 8*4 + 4*5=94

31. Problem 3: Optimal Binary Search Tree Input: Sorted list, with each element’s access frequency (how many times to be accessed/searched as a key over a period of time) Output: Optimal binary tree organization with minimal total cost –Every optimization problem optimizes an objective function: –Here it is total access cost Different tree organizations have different aggregate costs, –because the depths of the nodes are different on different tree. Problem: We want to find the optimal aggregate cost, and a corresponding bin-search tree.

32. Problem 3: Optimal Binary Search Tree Step 1 of DP: Formulate an objective function For our example list: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4) Objective function is: C(1, 5), cost for optimal tree for above list How many ways can it be broken to sub-trees? A i=3 C(1, i-1) C(i+1, 5) A 3 (5), ( A 1 (7), A 2 (10), ) ( A 4 (8), A 5 (4) )

33. A1A1 C(1, 1-1) C(1+1, 5) A2A2 C(1, 2-1) C(2+1, 5) (null left tree) A 1 (7) at root (A 2 (10), A 3 (5), A 4 (8), A 5 (4) on right) A 1 (7), A 2 (10), A 3 (5), A 4 (8), A 5 (4) (A 1 (7) left tree) A 2 (10) at root (A 3 (5), A 4 (8), A 5 (4) on right) How many such splits needed?

34. First i =1, A 1 (7), ( ) ( A 2 (10), A 3 (5), A 4 (8), A 5 (4) ) Next i= 3, A 3 (5), ( A 1 (7), A 2 (10) ) ( A 4 (8), A 5 (4) ) Next i= 2, A 2 (10), ( A 1 (7) ) ( A 3 (5),A 4 (8), A 5 (4) ) Next i= 4, A 4 (8), ( A 1 (7), A 2 (10), A 3 (5) ) ( A 5 (4) ) Last i= 5, A 5 (4) ( A 1 (7), A 2 (10), A 3 (5), A 4 (8) ) ( ) All values of i from 1 to 5 are to be tried, to find MINIMUM COST: C(1, 5)

35. A i (f i ) C(left, i-1) C(i+1, right) A 1 A 2 … A left … A i … A right … A n Generalize the Recurrence formulation for varying left and right pointers: C(l, r)  C(l, i-1) and C(i+1, r) For a choice of A i : C(l, r)  C(l, i-1) + C(i+1, r) +?

36. AiAi C(left, i-1) C(i+1, right) A 1 A 2 … A left … A i … A right … A n For a choice of A i we would like to write: C(l, r)  C(l, i-1) + C(i+1, r) + f i *1, l  i  r BUT,

37. C(stand alone left sub-tree) = 10*1 + 7*2 = 10 + 14 = 24 Cost = 5*1 + 10*2 + 7*3 + 8*2 + 4*3 = ….. + 41 + ….. But, A2(10) A1(7) A3(5) A2(10) A1(7) A4(8) A5(4)

38. AiAi C(left, i-1) C(i+1, right) A 1 A 2 … A left … A i … A right … A n Now Dynamic Programming does not work! C(l, i-1) and C(i+1, r) are no longer useful to compute C(l, r), unless …

39. C(stand alone left sub-tree) = 10*1 + 7*2 = 10 + 14 = 24 C (inside full tree) = 10*(1+1) + 7*(2+1), for 1 extra steps = 24 + (10*1 + 7*1) = 41 Cost = 5*1 + 10*2 + 7*3 + 8*2 + 4*3 = ….. + 41 + ….. Observe: A2(10) A1(7) A3(5) A2(10) A1(7) A4(8) A5(4)

40. C(stand alone left sub-tree) = 10*1 + 7*2 = 10 + 14 = 24 C (inside full tree) = 10*(1+1) + 7*(2+1), for 1 extra steps = 24 + (10 + 7) = C(stand-alone) + (sum of node costs) We can make DP work by reformulating the recurrence! Cost = 5*1 + 10*2 + 7*3 + 8*2 + 4*3 = ….. + 41 + ….. Generalize: A2(10) A1(7) A3(5) A2(10) A1(7) A4(8) A5(4)

41. Recurrence for Optimal Binary Search Tree If the i-th node is chosen as the root for this sub-tree, then C(l, r) = min[l  i  r] { f(i) + C(l, i-1) + C(i+1, r) +  j=l i-1  f(j) [additional cost for left sub-tree] +  j=i+1 r f(j) }[additional cost for right sub-tree] = min[l  i  r] {  j=l r f(j) + C(l, i-1) + C(i+1, r)}

42. Recurrence for Optimal Binary Search Tree If the i-th node is chosen as the root for this sub-tree, then C(l, r) = min[l  i  r] { f(i) + C(l, i-1) + C(i+1, r) +  j=l i-1  f(j) [additional cost for left sub-tree] +  j=i+1 r f(j) }[additional cost for right sub-tree] = min[l  i  r] {  j=l r f(j) + C(l, i-1) + C(i+1, r)} Recurrence termination? –Observe in the formula, which boundary values you will need. Final result in C(1, n). Start from zero element sub-tree (size=0), and gradually increase size, Finish when size= n, for the full tree

43. Optimal Binary Search Tree (Continued) Like matrix-chain multiplication-ordering we will develop a triangular part of the cost matrix (r>= l), and we will develop it diagonally (r = l + size), with varying size Note that our boundary condition, c(l, r)=0 if l > r (meaningless cost): This is recurrence termination We start from, l = r: single node trees (not with l=r-1: pairs of matrices, as in matrix-chain-mult case). Also, i now goes from ‘left’ through ‘right,’ and i is excluded from both the subtrees’ C’s.

44. Optimal Binary-search Tree Organization problem (Example) r ->12345 l=1 l=20 l=300 l=4000 l=50000 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Initialize:

45. r ->12345 l=17 l=2010 l=3005 l=40008 l=500004 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Diagonals: C(1, 1)=7, C(2, 2)=10, …. Singlets Optimal Binary-search Tree Organization problem (Example)

46. r ->12345 l=17* l=2010 l=3005 l=40008 l=500004 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Diagonals: C(1, 1)=7, C(2, 2)=10, …. C(1,2)=min{ i=1 C(1,0)+C(2,2)+f1+f2=0+10+17, Optimal Binary-search Tree Organization problem (Example)

47. r ->12345 l=17* l=2010 l=3005 l=40008 l=500004 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Diagonals: C(1, 1)=7, C(2, 2)=10, …. C(1,2)=min{ i=1 C(1,0)+C(2,2)+f1+f2=0+10+17, i=2 C(1,1) + C(3,2) + f1+f2 = 7 + 0 + 17} Optimal Binary-search Tree Organization problem (Example)

48. Write the DP algorithm for Optimal Binary-search Tree Organization problem r ->12345 l=1724(2) l=2010 l=3005 l=40008 l=500004 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Diagonals: C(1, 1)=7, C(2, 2)=10, …. C(1,2)=min{ i=1 C(1,0)+C(2,2)+f1+f2=0+10+17, i=2 C(1,1) + C(3,2) + f1+f2 = 7 + 0 + 17} = min{27, 24} = 24 (i=2)

49. Write the DP algorithm for Optimal Binary-search Tree Organization problem r ->12345 l=1724(2)345567 l=2010204151 l=30051826 l=4000816 l=500004 Keys: A 1 (7), A 2 (10), A 3 (5), A 4 (8), and A 5 (4). Diagonals: C(1, 1)=7, C(2, 2)=10, …. C(1,2)=min{ i=1 C(1,0)+C(2,2)+f1+f2=0+10+17, i=2 C(1,1) + C(3,2) + f1+f2 = 7 + 0 + 17} = min{27, 24} = 24 (i=2) Usual questions: How to keep track for finding optimum tree? Full Algorithm?

50. Problem4: All Pairs Shortest Path A variation of Djikstra’s algorithm. Called Floyd-Warshal’s algorithm. Good for dense graph. Algorithm Floyd // NOT A GOOD STYLE – WHY? Copy the distance matrix in d[1..n][1..n]; for k=1 through n do //consider each vertex as updating candidate for i=1 through n do for j=1 through n do if (d[i][k] + d[k][j] < d[i][j]) then d[i][j] = d[i][k] + d[k][j]; path[i][j] = k; // last updated via k End algorithm. Time: O(n 3 ), for 3 loops.Space: ? Cs.fit.edu/~dmitra/ Algorithms/lectures/ FloydExampleKormenPg696.pdf

51. Problem 5: DNA sequence Alignment (Approximate string matching) Score: 9 matches times 1 1 mismatch times (-1) 1 gap times (-2) = 6 Find a best-score alignment Source: Setubal & Meidanis, Bioinformatics

52. Problem 5: DNA sequence Alignment s 1 s 2 s 3 …… s n t 1 t 2 t 3 ……………..t m

53. Problem 5: DNA sequence Alignment Note, initialization, Or, Recurrence termination Alignment: start from (n,m)-corner, Stops at (0,0) corner

54. Problem 5: Gene Alignment

55. Problem 5-1: Gene Alignment, local  Global alignment We may want Local alignment 

56. Problem 6-1: Gene Alignment, local We may want Local alignment  Initialize with 0’s. Alignment, starts from highest value on the table, And stops with a zero  No negative score